Biology subjects

Ceze, L.

Publications and source records attributed to Ceze, L..

6 recordsLinked to original sources

bioRxiv2021

A nanopore interface for high bandwidth DNA computing

DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies MinION device). We show that engineered reporter probes can be detected and classified with high accuracy at the single-molecule level directly from raw nanopore signals using deep learning. We then demonstrate this methods utility in multiplexed detection of clinically relevant microRNA sequences. These results increase DSD output bandwidth by an order of magnitude over what is possible with fluorescence spectroscopy, laying the foundations for a new paradigm in DNA circuit readout and programmable multiplexed molecular diagnostics using portable nanopore devices.

bioengineering↗

bioRxiv2019

Multiplexed direct detection of barcoded protein reporters on a nanopore array

Genetically encoded reporter proteins are a cornerstone of molecular biology. While they are widely used to measure many biological activities, the current number of uniquely addressable reporters that can be used together for one-pot multiplexed tracking is small due to overlapping detection channels such as fluorescence. To address this, we built an expanded library of orthogonally-barcoded Nanopore-addressable protein Tags Engineered as Reporters (NanoporeTERs), which can be read and demuxed by nanopore sensors at the single-molecule level. By adapting a commercially available nanopore sensor array platform typically used for real-time DNA and RNA sequencing (Oxford Nanopore Technologies MinION), we show direct detection of NanoporeTER expression levels from unprocessed bacterial culture with no specialized sample preparation. These results lay the foundations for a new class of reporter proteins to enable multiplexed, real-time tracking of gene expression with nascent nanopore sensor technology.

synthetic biology↗

bioRxiv2019

Experimental Assessment of PCR Specificity and Copy Number for Reliable Data Retrieval in DNA Storage

Synthetic DNA has been gaining momentum as a potential storage medium for archival data storage1-9. Digital information is translated into sequences of nucleotides and the resulting synthetic DNA strands are then stored for later individual file retrieval via PCR7-9 (Fig. 1a). Using a previously presented encoding scheme9 and new experiments, we demonstrate reliable file recovery when as few as 10 copies per sequence are stored, on average. This results in density of about 17 exabytes/g, nearly two orders of magnitude greater than prior work has shown6. Further, no prior work has experimentally demonstrated access to specific files in a pool more complex than approximately 106 unique DNA sequences9, leaving the issue of accurate file retrieval at high data density and complexity unexamined. Here, we demonstrate successful PCR random access using three files of varying sizes in a complex pool of over 1010 unique sequences, with no evidence that we have begun to approach complexity limits. We further investigate the role of file size on successful data recovery, the effect of increasing sequencing coverage to aid file recovery, and whether DNA strands drop out of solution in a systematic manner. These findings substantiate the robustness of PCR as a random access mechanism in complex settings, and that the number of copies needed for data retrieval does not compromise density significantly.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC=\"FIGDIR/small/565150_fig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@4b79a7org.highwire.dtl.DTLVardef@11fca45org.highwire.dtl.DTLVardef@18b830org.highwire.dtl.DTLVardef@e47101_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO (a) A high-level representation of the DNA data storage pipeline. (b) (Left) The bar chart depicts contents of the initial, undiluted pool. (Right) The illustration shows the serial nature of subsequent dilutions. Mean copy number refers to the mean number of copies of each files unique sequences as determined by qPCR (Supplemental Section 1). One serial dilution used water as the diluent in each step; the other used a solution of 150Nmers to dilute the pool to much greater complexity. (c) Details of how the samples were diluted. Note that the dilution steps were identical regardless of diluent. The smallest percent of pool accessed is calculated by dividing the size of the smallest file by the number of unique sequences in the 1 {micro}L of solution used for PCR random access. This percentage refers to the 150N diluent pool since the small file in the water diluent pool is a constant 0.13%.\n\nC_FIG

synthetic biology↗

bioRxiv2019

Quantifying Molecular Bias in DNA Data Storage

DNA has recently emerged as an attractive medium for future digital data storage because of its extremely high information density and potential longevity. Recent work has shown promising results in developing proof-of-principle prototype systems. However, very uneven (biased) sequencing coverage distributions have been reported, which indicates inefficiencies in the storage process and points to optimization opportunities. These deviations from the average coverage in oligonucleotide copy distribution result in sequence drop-out and make error-free data retrieval from DNA more challenging. The uneven copy distribution was believed to stem from the underlying molecular processes, but the interplay between these molecular processes and the copy number distribution has been poorly understood until now. In this paper, we use millions of unique sequences from a DNA-based digital data archival system to study the oligonucleotide copy unevenness problem and show that two important sources of bias are the synthesis process and the Polymerase Chain Reaction (PCR) process. By mapping the sequencing coverage of a large complex oligonucleotide pool back to its spatial distribution on the synthesis chip, we find that significant bias comes from array-based oligonucleotide synthesis. We also find that PCR stochasticity is another main driver of oligonucleotide copy variation. Based on these findings, we develop a statistical model for each molecular process as well as the overall process and compare the predicted bias with our experimental data. We further use our model to explore the trade-offs between synthesis bias, storage physical density and sequencing redundancy, providing insights for engineering efficient, robust DNA data storage systems.

synthetic biology↗

bioRxiv2018

Exploiting Index Cross-Talk to Modify Variant Calls

Modern next-generation DNA sequencers support multiplex sequencing to improve throughput and decrease costs. This is done by pooling and sequencing samples together in parallel, which are later demultiplexed according to their unique indexes1, 2. When reads are assigned to the wrong index, called index cross-talk, information is leaked between samples3-6. This creates a physical information side-channel, a well known class of vulnerabilities in information security7-10, that may be used to modify downstream results. Here we demonstrate the feasibility of such an attack through the use of a separately indexed library that causes a wild-type human exome to be misclassified as heterozygous at the sickle-cell locus. Simple methods can be used to minimize or detect attempts to modify genetic variants using this side-channel, such as filtering by read quality or finding outliers in read coverage. To further minimize this risk we recommend the use of new library preparation methods that reduce index cross-talk, like unique dual indexes11, 12, whenever samples are sequenced together in important applications. Biotechnology that interfaces molecular and digital information, like DNA sequencers, may have security risks typically associated with information systems, including the side-channel vulnerability described in this study. We encourage the community to consider the security of genomics-information pipelines before they reach mass adoption.

bioengineering↗

bioRxiv2017

Scaling up DNA data storage and randomaccess retrieval

Current storage technologies can no longer keep pace with exponentially growing amounts of data. 1 Synthetic DNA offers an attractive alternative due to its potential information density of ~ 1018 B/mm3, 107 times denser than magnetic tape, and potential durability of thousands of years.2 Recent advances in DNA data storage have highlighted technical challenges, in particular, coding and random access, but have stored only modest amounts of data in synthetic DNA. 3,4,5 This paper demonstrates an end-to-end approach toward the viability of DNA data storage with large-scale random access. We encoded and stored 35 distinct files, totaling 200MB of data, in more than 13 million DNA oligonucleotides (about 2 billion nucleotides in total) and fully recovered the data with no bit errors, representing an advance of almost an order of magnitude compared to prior work. 6 Our data curation focused on technologically advanced data types and historical relevance, including the Universal Declaration of Human Rights in over 100 languages,7 a high-definition music video of the band OK Go,8 and a CropTrust database of the seeds stored in the Svalbard Global Seed Vault.9 We developed a random access methodology based on selective amplification, for which we designed and validated a large library of primers, and successfully retrieved arbitrarily chosen items from a subset of our pool containing 10.3 million DNA sequences. Moreover, we developed a novel coding scheme that dramatically reduces the physical redundancy (sequencing read coverage) required for error-free decoding to a median of 5x, while maintaining levels of logical redundancy comparable to the best prior codes. We further stress-tested our coding approach by successfully decoding a file using the more error-prone nanopore-based sequencing. We provide a detailed analysis of errors in the process of writing, storing, and reading data from synthetic DNA at a large scale, which helps characterize DNA as a storage medium and justify our coding approach. Thus, we have demonstrated a significant improvement in data volume, random access, and encoding/decoding schemes that contribute to a whole-system vision for DNA data storage.

bioengineering↗